Contacts of the strand formed by residues 26 - 34 (chain D) in PDB entry 1I5L
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 26 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D ILE* 3.7 18.0 - - + +
19D VAL 3.6 10.3 - - - +
20D ARG* 3.3 39.8 + - - +
24D GLY 3.4 3.2 + - - +
25D ARG* 1.3 72.4 - - - +
27D PHE* 1.3 75.5 + - - +
28D ARG* 5.4 0.7 - - - +
47D GLU* 3.4 3.5 - - - +
48D ILE* 2.9 52.5 + - + +
69D PHE* 5.9 0.4 - - - -
55E ARG* 2.9 32.2 + - - -
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Residues in contact with PHE 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C PHE* 3.4 45.3 - + - -
17D VAL 3.8 0.4 - - - +
18D ILE* 3.2 8.1 - - - +
19D VAL* 2.9 35.7 + - + +
21D LEU* 4.1 21.8 - - + -
25D ARG* 5.0 2.5 - - + -
26D GLU* 1.3 88.4 - - - +
28D ARG* 1.3 62.3 + - - +
42D LEU* 4.0 15.9 - - + -
45D ALA* 4.2 13.5 - - + -
46D GLU 3.2 17.5 - - - -
47D GLU* 4.2 23.1 - - + -
48D ILE* 5.0 0.2 - - - -
57D VAL* 4.6 9.4 - - + -
60D VAL* 4.3 21.8 - - + -
62D ILE* 4.1 14.8 - - + -
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Residues in contact with ARG 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D VAL 3.4 4.5 - - - +
18D ILE* 3.0 47.3 - - + +
26D GLU* 5.4 0.9 - - - -
27D PHE* 1.3 80.9 - - - +
29D GLY* 1.3 57.9 + - - +
42D LEU* 5.3 0.2 - - - -
44D ASP 3.9 0.7 - - - +
45D ALA* 2.8 26.1 - - - -
46D GLU* 2.9 30.4 + - - +
48D ILE* 3.1 29.6 - - + -
73D ALA* 3.9 14.2 - - - +
74D PRO* 4.9 7.7 - - - +
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Residues in contact with GLY 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D PRO* 3.3 6.1 - - - +
17D VAL* 2.7 36.3 + - - +
27D PHE 4.3 0.2 - - - -
28D ARG* 1.3 76.2 - - - +
30D THR* 1.3 60.6 + - - -
42D LEU* 4.3 8.0 - - - +
43D LEU 3.8 10.5 - - - -
44D ASP 3.8 6.1 - - - -
45D ALA* 3.9 6.1 - - - -
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Residues in contact with THR 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LYS* 3.2 39.2 + - - +
15D SER 3.5 7.1 + - - -
16D PRO* 4.3 4.7 - - - +
29D GLY* 1.3 72.7 - - - -
31D LEU* 1.3 64.0 + - - +
32D ASP* 3.0 9.3 + - - +
42D LEU* 3.3 4.0 - - - -
43D LEU* 2.9 48.5 + - + +
44D ASP* 5.9 0.7 - - - +
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Residues in contact with LEU 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 3.9 43.3 - - + +
12D SER* 3.9 17.0 - - - +
13D LEU* 3.7 12.2 - - + -
14D LYS* 3.0 26.2 + - - -
15D SER 3.2 7.3 + - - -
17D VAL* 4.0 22.2 - - + +
29D GLY 3.8 2.6 + - - -
30D THR* 1.3 67.7 - - - +
32D ASP* 1.3 59.9 - - - +
33D GLY 3.1 26.9 - - - +
34D TYR* 4.7 4.0 - - + -
40D LEU* 4.3 16.6 - - + -
41D VAL 3.6 9.9 - - - +
42D LEU* 3.9 11.8 - - + +
70D VAL* 5.3 2.0 - - + -
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Residues in contact with ASP 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C PRO 5.0 2.6 - - - +
3C PRO* 3.6 39.9 - - - +
8C VAL* 4.6 2.4 - - - +
11C ARG* 4.9 2.1 + - - -
13D LEU* 3.6 12.8 - - - +
14D LYS* 5.8 0.4 - - - +
30D THR* 3.0 4.6 + - - +
31D LEU* 1.3 73.7 - - - +
33D GLY* 1.3 56.2 + - - +
41D VAL* 2.7 32.8 + - + +
43D LEU* 3.6 37.2 - - + +
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Residues in contact with GLY 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C PRO 3.9 15.5 - - - -
5C PRO* 3.8 7.6 - - - -
13D LEU* 4.1 7.6 - - - -
31D LEU* 3.1 18.2 - - - +
32D ASP* 1.3 80.4 - - - +
34D TYR* 1.3 68.9 + - - +
40D LEU* 3.9 0.2 - - - -
41D VAL* 3.3 20.4 + - - +
52K GLU* 4.5 0.7 - - - -
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Residues in contact with TYR 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C PRO 4.7 0.4 + - - -
4C ARG* 2.6 31.0 + - - -
5C PRO* 3.3 14.8 - - - +
6D LEU* 3.7 24.0 + - + +
9D LEU* 4.0 18.6 - - + -
10D ASN* 3.1 51.7 + - + +
13D LEU* 3.9 16.4 - - + -
31D LEU* 4.7 3.6 - - + -
33D GLY* 1.3 73.5 - - - +
35D ASP* 1.3 66.8 + - - +
36D ILE* 6.3 0.9 - - + -
39D ASN 3.4 17.3 - - - +
40D LEU* 4.0 11.7 - - + -
49K GLN* 4.2 5.2 + - - -
52K GLU* 2.7 37.6 + - - +
54K VAL* 5.0 1.4 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il